although after making this post I did end up getting the full tree working using separate refineries for each step (3), and just used blank single pipes on each input and output not being used.
The third step one though currently is difficult to use since you need an infinite source of nitrogen as well as the chemical building needing a duplicant, so sour gas either has to be dumped to space or chilled to methane.
I'm guessing there should be a recipe somewhere to split the ammonia to nitrogen and hydrogen?

seconding this, I keep finding 10 ton per tile pools of ammonia, but there's if you're lucky only like 500kg of nitrogen on a big map

Seems nitrogen is renewable from space mining, leaving the small amounts on the asteroid as a tease I guess
processing all the nitrogen into nitric and then using it to process regolith gave me 1kg of niobium and 72kg of high grade left over

Don't worry about this, the building will totally reworked and released again. Like the new Crude Oil Refinery I will split its functions in to other buildings instead of doing everything in one.

@Ronivan Did you implement this rework in the current version or is still WIP?

Originally posted by Diablo7:

@Ronivan Did you implement this rework in the current version or is still WIP?

It is in the current version, although a bit tricky to get working currently as the output sour and polluted waters are above boiling point if the steam, oil and raw gas are all hot, but one method is to cool the oil and raw gas to around 0C.
I would more expect the water's to be the temperature of the buildings themselves, but that still requires cooling the buildings so not a huge difference in setup.

Originally posted by Vectrobe:

Originally posted by Diablo7:

@Ronivan Did you implement this rework in the current version or is still WIP?

It is in the current version, although a bit tricky to get working currently as the output sour and polluted waters are above boiling point if the steam, oil and raw gas are all hot, but one method is to cool the oil and raw gas to around 0C.
I would more expect the water's to be the temperature of the buildings themselves, but that still requires cooling the buildings so not a huge difference in setup.

Thanks for your answer.